Libyan officials were deeply concerned in 2011, as Secretary of State Hillary Rodham Clinton was trying to remove Moammar Gadhafi from power, that weapons were being funneled to NATO-backed rebels with ties to al Qaeda, fearing that well-armed insurgents could create a safe haven for terrorists, according to secret intelligence reports obtained by The Washington Times.

The reports included a 16-page list of weapons that Libyans supposedly tracked to the rebels from Western sources or their allies in the region. The memos were corroborated by a U.S. intelligence asset familiar with the documents as well as former top Gadhafi regime official Mohammed Ismael.

“NATO has given permission to a number of weapons-loaded aircraft to land at Benghazi airport and some Tunisian airports,” the intelligence report said, identifying masses of weapons including tanks and surface-to-air missiles.

That report, which was prepared in English so it could be passed by a U.S. intelligence asset to key members of Congress, identified specific air and sea shipments observed by Libyan intelligence moving weapons to the rebels trying to unseat the Gadhafi regime.

“There is a close link between al Qaeda, Jihadi organizations, and the opposition in Libya,” the report warned.

In the documents and separately recorded conversations with U.S. emissaries, Libyan officials expressed particular concern that the weapons and training given the rebels would spread throughout the region, in particular turning the city of Benghazi into a future terrorist haven.

Those fears would be realized a little over a year later when a band of jihadist insurgents attacked the State Department diplomatic post in Benghazi and a related CIA compound, killing four Americans including Ambassador J. Christopher Stevens. Today, more than three years after Gadhafi fell from power and was killed, Benghazi and much of the rest of Libya remain in chaos, riddled with violence among rival tribes and thriving jihadi groups.

Mrs. Clinton, now considering a run for president, was the moving force inside the Obama administration to encourage U.S. military intervention to unseat Gadhafi in Libya. The latest documents and audio recordings are likely to give her Republican critics on Capitol Hill fresh ammunition to question whether she had an adequate plan and whether her efforts led to the tragedy in Benghazi a year later and the general lawlessness and chaos that have gripped Libya since.

The Times reported last week that U.S. intelligence did not support the story that Mrs. Clinton used to sell the war in Libya, mainly that there was an imminent danger of a genocide to be carried out by the Gadhafi regime. The intelligence community, in fact, had come to the opposite conclusion: that Gadhafi would not risk world outrage by killing civilians en masse even as he tried to crush the rebellion in his country.

The Times also reported that the Pentagon and a key Democrat so distrusted Mrs. Clinton’s decision-making on Libya that they opened their own secret diplomatic conversations with the Gadhafi regime, going around the State Department.

In one conversation recorded in summer 2011 between Libyan officials and an intelligence asset dispatched by the Pentagon as a back-door channel, the asset told Mr. Ismael, who served then as Gadhafi’s chief of staff, that U.S. officials were considering taking some of the Libyan dictator’s frozen money assets and sending it to the rebels.

“I’m in contact with some of the people over in Benghazi and they’ve told me point blank that their first use of this money is, is to buy military training, weapons and mercenaries,” the Pentagon intelligence asset told Mr. Ismael on July 24, 2011.

In a separate conversation with Dennis J. Kucinich, an Ohio Democrat serving in the House, Gadhafi’s eldest son, Seif, told the congressman that Libyan intelligence had observed Qatar, a major U.S. ally in the region, facilitating weapons shipments. Qatar has steadfastly and repeatedly denied arming the rebels.

“The Qataris have spent more than $100 million on this, and they have an agreement with the rebels that the moment you rule Libya you pay us back,” Seif Gadhafi told Mr. Kucinich in a conversation recorded in May 2011.

“So, it’s your position that your government has been trying to defend itself against an insurrection brought about by jihadists who were joined by gangsters, terrorists and that there’s basically about 1,000 people who were joined by NATO?” Mr. Kucinich asked.

“Yes,” Seif Gadhafi replied.

“You’re saying that this relates to internal matters, matters internal to the region relating of a power struggle in which they then turned their attention to Libya to try to engulf Libya in their own desire for increasing their power?” Mr. Kucinich asked.

“For the Qataris, they are doing this with every country, with every country,” Mr. Gadhafi said. “This is their plan, I mean in public. This is their own agenda. I mean, it’s not something hidden, or something, you know, private. But now, we have, and plus the French and British have also have their own agenda, you know, commercial interests, political interests, they have their own interests. They told us, especially the French, and the Qataris and the British: We want those people to share the power with you, our own people, the heads of rebels.”

The recorded conversations also included concerns that the U.S. might try to arm the rebels despite a U.N. arms embargo on Libya.

On March 27, 2011, days after the intervention began, Mrs. Clinton argued that the arms embargo could be disregarded if shipping weapons to rebels would help protect civilians, but defense officials in the United Kingdom disagreed with her interpretation of international law.

“We’re not arming the rebels. We’re not planning to arm the rebels,” British Defense Secretary Liam Fox told the BBC the day Mrs. Clinton hinted otherwise.

Likewise, Qatari officials sent a letter Feb. 2, 2012, to the United Nations about the Libyan uprising, “categorically” denying that they had “supplied the revolutionaries with arms and ammunitions” as some had reported.

Attempts to contact the Qatari Embassy in Washington for comment Sunday were unsuccessful, but the classified Libyan intelligence report indicates that Qatar sent tanks, missiles, trucks and military advisers to the rebels.

Distrust between Libya and Qatar had simmered for years before the civil war in Libya erupted. Mr. Ismael told The Times in an interview that the Qataris had a grudge against the Gadhafi regime because it did not give them natural gas and oil concessions that were promised in 2007.

The Libyan intelligence reports provided to the Pentagon’s emissary detailed specific weapons shipments they said came from Qatar.

“On 15th of March the ship loaded with arm[s] arrived to the seaport of Tobruk. On 4th April 2011 two Qatari aircraft laden with a number of tanks, [ground-attack] missiles and heavy trucks was arranged. On 11th April 2011 a number of boats departed Benghazi for Misrata, the shipment comprised assistance including SAM-7 [anti-aircraft] missiles. On 22nd April 2011, 800 rifles were sent from Benghazi to Misrata,” the report said.

Whether such shipments were supposed to stay with NATO or go to the rebels remains in dispute. But academic analysts say the Libyan concerns that arming the rebels would benefit terrorists were shared widely.

NATO allies knew of the dangerous jihadi elements operating in Benghazi before the 2011 intervention began, according to Noman Benotman, president of the British-based Quilliam Foundation, a think tank dedicated to combating Islamic extremism.

Mr. Benotman also was a leader of the Libyan Islamic Fighting Group but left the organization prior to the 2011 revolution.

“A lot of jihadists that had been locked up by the regime were released after the revolution started. They picked up many of the guns that were coming into the country and fought, but they were not fighting for democracy — they were fighting their own revolution, trying to build a state based on a vicious, violent, radical, Islamic ideology. They took advantage of the situation,” he said.

“There were pro-democracy demonstrators participating in the revolution, of course, but there was also crystal-clear evidence of jihadists and jihadist tactics in Benghazi before the NATO intervention started, so no one can say there were no jihadists there,” he said.